LDSC59 was used to estimate heritability of our five phenotypes for EAS and EUR ancestries using a standard 1-cM window size. For ancestries with more recent admixture (AFR and AMR ancestries), we used covariate-adjusted LDSC60 for the same analyses in which in-sample LD scores were calculated using ancestry-matched TOPMed reference samples and adjusted by the first 50 principal components. For more recently admixed AFR and AMR ancestries, which tend to show longer-range LD, we used a 20-cM window size when calculating LD scores. For both LDSC and covariate-adjusted LDSC, variants were subset to HapMap3 (ref. 61) with MAF > 0.05, as recommended for this approach.
